Nothing
R/celdaGridSearch.R
In celda: CEllular Latent Dirichlet Allocation
Defines functions
.subsetCeldaListSCE
.createSCEceldaGridSearch
.celdaGridSearch
#' @title Run Celda in parallel with multiple parameters
#' @description Run Celda with different combinations of parameters and
#' multiple chains in parallel. The variable \link{availableModels} contains
#' the potential models that can be utilized. Different parameters to be tested
#' should be stored in a list and passed to the argument \code{paramsTest}.
#' Fixed parameters to be used in all models, such as \code{sampleLabel}, can
#' be passed as a list to the argument \code{paramsFixed}. When
#' \code{verbose = TRUE}, output from each chain will be sent to a log file
#' but not be displayed in \code{stdout}.
#' @param x A numeric \link{matrix} of counts or a
#' \linkS4class{SingleCellExperiment}
#' with the matrix located in the assay slot under \code{useAssay}.
#' Rows represent features and columns represent cells.
#' @param useAssay A string specifying the name of the
#' \link{assay} slot to use. Default "counts".
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param model Celda model. Options available in \link{availableModels}.
#' @param paramsTest List. A list denoting the combinations of parameters to
#' run in a celda model. For example,
#' \code{list(K = seq(5, 10), L = seq(15, 20))}
#' will run all combinations of K from 5 to 10 and L from 15 to 20 in model
#' \link{celda_CG}.
#' @param paramsFixed List. A list denoting additional parameters to use in
#' each celda model. Default NULL.
#' @param maxIter Integer. Maximum number of iterations of sampling to
#' perform. Default 200.
#' @param nchains Integer. Number of random cluster initializations. Default 3.
#' @param cores Integer. The number of cores to use for parallel estimation of
#' chains. Default 1.
#' @param bestOnly Logical. Whether to return only the chain with the highest
#' log likelihood per combination of parameters or return all chains. Default
#' TRUE.
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. Seed values
#' \code{seq(seed, (seed + nchains - 1))} will be supplied to each chain in
#' \code{nchains}. If NULL, no calls to
#' \link[withr]{with_seed} are made.
#' @param perplexity Logical. Whether to calculate perplexity for each model.
#' If FALSE, then perplexity can be calculated later with
#' \link{resamplePerplexity}. Default TRUE.
#' @param verbose Logical. Whether to print log messages during celda chain
#' execution. Default TRUE.
#' @param logfilePrefix Character. Prefix for log files from worker threads
#' and main process. Default "Celda".
#' @return A \linkS4class{SingleCellExperiment} object. Function
#' parameter settings and celda model results are stored in the
#' \link{metadata} \code{"celda_grid_search"} slot.
#' @param ... Ignored. Placeholder to prevent check warning.
#' @seealso \link{celda_G} for feature clustering, \link{celda_C} for
#' clustering of cells, and \link{celda_CG} for simultaneous clustering of
#' features and cells. \link{subsetCeldaList} can subset the \code{celdaList}
#' object. \link{selectBestModel} can get the best model for each combination
#' of parameters.
#' @import foreach
#' @importFrom doParallel registerDoParallel
#' @importFrom methods is
#' @examples
#' \dontrun{
#' data(celdaCGSim)
#' ## Run various combinations of parameters with 'celdaGridSearch'
#' celdaCGGridSearchRes <- celdaGridSearch(celdaCGSim$counts,
#' model = "celda_CG",
#' paramsTest = list(K = seq(4, 6), L = seq(9, 11)),
#' paramsFixed = list(sampleLabel = celdaCGSim$sampleLabel),
#' bestOnly = TRUE,
#' nchains = 1,
#' cores = 1)
#' }
#' @export
setGeneric("celdaGridSearch", function(x, ...) {
standardGeneric("celdaGridSearch")})
#' @rdname celdaGridSearch
#' @export
setMethod("celdaGridSearch",
signature(x = "SingleCellExperiment"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
model,
paramsTest,
paramsFixed = NULL,
maxIter = 200,
nchains = 3,
cores = 1,
bestOnly = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfilePrefix = "Celda") {
xClass <- "SingleCellExperiment"
if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {
stop(altExpName, " not in 'altExpNames(x)'. Run ",
"selectFeatures(x) first!")
}
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {
stop(useAssay, " not in assayNames(altExp(x, altExpName))")
}
counts <- SummarizedExperiment::assay(altExp, i = useAssay)
celdaList <- .celdaGridSearch(counts = counts,
model = paste0(".", model),
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
altExp <- .createSCEceldaGridSearch(celdaList = celdaList,
sce = altExp,
xClass = xClass,
useAssay = useAssay,
model = model,
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
seed = seed,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
})
#' @rdname celdaGridSearch
#' @export
setMethod("celdaGridSearch",
signature(x = "matrix"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
model,
paramsTest,
paramsFixed = NULL,
maxIter = 200,
nchains = 3,
cores = 1,
bestOnly = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfilePrefix = "Celda") {
ls <- list()
ls[[useAssay]] <- x
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)
SingleCellExperiment::altExp(sce, altExpName) <- sce
xClass <- "matrix"
celdaList <- .celdaGridSearch(counts = x,
model = paste0(".", model),
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
altExp <- .createSCEceldaGridSearch(celdaList = celdaList,
sce = SingleCellExperiment::altExp(sce, altExpName),
xClass = xClass,
useAssay = useAssay,
model = model,
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
seed = seed,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
SingleCellExperiment::altExp(sce, altExpName) <- altExp
return(sce)
})
.celdaGridSearch <- function(counts,
model,
paramsTest,
paramsFixed,
maxIter,
nchains,
cores,
bestOnly,
seed,
perplexity,
verbose,
logfilePrefix) {
## Check parameters
.validateCounts(counts)
modelParams <- as.list(formals(model))
if (!all(names(paramsTest) %in% names(modelParams))) {
badParams <- setdiff(names(paramsTest), names(modelParams))
stop(
"The following elements in 'paramsTest' are not arguments of '",
substring(model, 2),
"': ",
paste(badParams, collapse = ",")
)
}
if (!is.null(paramsFixed) &&
!all(names(paramsFixed) %in% names(modelParams))) {
badParams <- setdiff(names(paramsFixed), names(modelParams))
stop(
"The following elements in 'paramsFixed' are not arguments",
" of '",
substring(model, 2),
"': ",
paste(badParams, collapse = ",")
)
}
modelParamsRequired <- setdiff(
names(modelParams[modelParams == ""]),
"counts"
)
if (!all(modelParamsRequired %in% c(
names(paramsTest),
names(paramsFixed)
))) {
missing.params <- setdiff(
modelParamsRequired,
c(names(paramsTest), names(paramsFixed))
)
stop(
"The following arguments are not in 'paramsTest' or 'paramsFixed'",
" but are required for '",
substring(model, 2),
"': ",
paste(missing.params, collapse = ",")
)
}
if (any(c("z.init", "y.init", "sampleLabel") %in% names(paramsTest))) {
stop(
"Setting parameters such as 'z.init', 'y.init', and 'sampleLabel'",
" in 'paramsTest' is not currently supported."
)
}
if (any(c("nchains") %in% names(paramsTest))) {
warning(
"Parameter 'nchains' should not be used within the paramsTest",
" list"
)
paramsTest[["nchains"]] <- NULL
}
# Pre-generate a set of random seeds to be used for each chain
if (is.null(seed)) {
allSeeds <- NULL
} else {
allSeeds <- seq(seed, (seed + nchains - 1))
}
# Set up parameter combinations for each individual chain
runParams <- base::expand.grid(c(
chain = list(seq_len(nchains)),
paramsTest
))
runParams <- cbind(index = seq_len(nrow(runParams)), runParams)
if (is.null(allSeeds)) {
runParams <- cbind(runParams,
seed = rep("NULL", nrow(runParams)))
} else {
runParams <- cbind(runParams,
seed = rep(allSeeds, nrow(runParams) / nchains))
}
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = FALSE,
verbose = verbose
)
.logMessages("Starting celdaGridSearch with",
substring(model, 2),
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages("Number of cores:",
cores,
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = TRUE,
verbose = verbose
)
startTime <- Sys.time()
# An MD5 checksum of the count matrix. Passed to models so
# later on, we can check on celda_* model objects which
# count matrix was used.
counts <- .processCounts(counts)
countChecksum <- .createCountChecksum(counts)
## Use DoParallel to loop through each combination of parameters
cl <- parallel::makeCluster(cores)
doParallel::registerDoParallel(cl)
i <- NULL # Setting visible binding for R CMD CHECK
resList <- foreach(
i = seq_len(nrow(runParams)),
.export = model,
.combine = c,
.multicombine = TRUE
) %dopar% {
## Set up chain parameter list
current.run <- c(runParams[i, ])
chainParams <- list()
for (j in names(paramsTest)) {
chainParams[[j]] <- current.run[[j]]
}
chainParams$counts <- counts
chainParams$maxIter <- maxIter
chainParams$nchain <- 1
chainParams$countChecksum <- countChecksum
chainParams$verbose <- verbose
chainParams$logfile <- paste0(
logfilePrefix,
"_",
paste(paste(
colnames(runParams), runParams[i, ],
sep = "-"
), collapse = "_"),
"_Seed-",
ifelse(is.null(chainParams$seed), "NULL", chainParams$seed),
"_log.txt"
)
## Run model
if (is.null(seed)) {
res <- do.call(model, c(chainParams, paramsFixed))
} else {
chainSeed <- allSeeds[ifelse(i %% nchains == 0,
nchains, i %% nchains)]
res <- with_seed(chainSeed,
do.call(model, c(chainParams, paramsFixed)))
}
return(list(res))
}
parallel::stopCluster(cl)
logliks <- vapply(resList, function(mod) {
bestLogLikelihood(mod)
}, double(1))
runParams <- cbind(runParams, logLikelihood = logliks)
celdaRes <- methods::new(
"celdaList",
runParams = runParams,
resList = resList,
countChecksum = countChecksum
)
if (isTRUE(bestOnly)) {
celdaRes <- selectBestModel(celdaRes, asList = TRUE)
}
if (isTRUE(perplexity)) {
.logMessages(
date(),
".. Calculating perplexity",
append = TRUE,
verbose = verbose,
logfile = NULL
)
celdaRes <- resamplePerplexity(counts, celdaRes, seed = seed)
}
endTime <- Sys.time()
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages("Completed celdaGridSearch. Total time:",
format(difftime(endTime, startTime)),
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = TRUE,
verbose = verbose
)
return(celdaRes)
}
#' @title Subset celda model from SCE object returned from
#' \code{celdaGridSearch}
#' @description Select a subset of models from a
#' \linkS4class{SingleCellExperiment} object generated by
#' \link{celdaGridSearch} that match the criteria in the argument
#' \code{params}.
#' @param x Can be one of
#' \itemize{
#' \item A \linkS4class{SingleCellExperiment} object returned from
#' \code{celdaGridSearch}, \code{recursiveSplitModule},
#' or \code{recursiveSplitCell}. Must contain a list named
#' \code{"celda_grid_search"} in \code{metadata(x)}.
#' \item celdaList object.}
#' @param params List. List of parameters used to subset the matching celda
#' models in list \code{"celda_grid_search"} in \code{metadata(x)}.
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return One of
#' \itemize{
#' \item A new \linkS4class{SingleCellExperiment} object containing
#' all models matching the
#' provided criteria in \code{params}. If only one celda model result in the
#' \code{"celda_grid_search"} slot in \code{metadata(x)} matches
#' the given criteria, a new \linkS4class{SingleCellExperiment} object
#' with the matching model stored in the
#' \link{metadata}
#' \code{"celda_parameters"} slot will be returned. Otherwise, a new
#' \linkS4class{SingleCellExperiment} object with the subset models stored
#' in the \link{metadata}
#' \code{"celda_grid_search"} slot will be returned.
#' \item A new \code{celdaList} object containing all models matching the
#' provided criteria in \code{params}. If only one item in the
#' \code{celdaList} matches the given criteria, the matching model will be
#' returned directly instead of a \code{celdaList} object.}
#' @seealso \link{celdaGridSearch} can run Celda with multiple parameters and
#' chains in parallel. \link{selectBestModel} can get the best model for each
#' combination of parameters.
#' @export
setGeneric("subsetCeldaList", function(x, ...) {
standardGeneric("subsetCeldaList")})
#' @rdname subsetCeldaList
#' @examples
#' data(sceCeldaCGGridSearch)
#' sceK5L10 <- subsetCeldaList(sceCeldaCGGridSearch,
#' params = list(K = 5, L = 10))
#' @export
setMethod("subsetCeldaList",
signature(x = "SingleCellExperiment"),
function(x, params, altExpName = "featureSubset") {
## Check for bad parameter names
if (!all(names(params) %in% colnames(runParams(x,
altExpName = altExpName)))) {
badParams <- setdiff(names(params),
colnames(runParams(x, altExpName = altExpName)))
stop("The following elements in 'params' are not columns in",
" runParams(x, altExpName = altExpName) ",
paste(badParams, collapse = ",")
)
}
## Subset 'runParams' based on items in 'params'
newRunParams <- runParams(x, altExpName = altExpName)
for (i in names(params)) {
newRunParams <-
subset(newRunParams, newRunParams[, i] %in% params[[i]])
if (nrow(newRunParams) == 0) {
stop("No runs matched the criteria given in 'params'. Check",
" 'runParams(x, altExpName = altExpName)' for complete",
" list of parameters used",
" to generate 'x'.")
}
}
## Get index of selected models, subset celdaList, and return
ix <- match(newRunParams$index, runParams(x,
altExpName = altExpName)$index)
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (length(ix) == 1) {
altExp <- .subsetCeldaListSCE(altExp, ix)
} else {
altExp@metadata$celda_grid_search@runParams <-
as.data.frame(newRunParams)
altExp@metadata$celda_grid_search@resList <-
altExp@metadata$celda_grid_search@resList[ix]
}
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname subsetCeldaList
#' @examples
#' data(celdaCGGridSearchRes)
#' resK5L10 <- subsetCeldaList(celdaCGGridSearchRes,
#' params = list(K = 5, L = 10))
#' @export
setMethod("subsetCeldaList",
signature(x = "celdaList"),
function(x, params) {
## Check for bad parameter names
if (!all(names(params) %in% colnames(runParams(x)))) {
badParams <- setdiff(names(params), colnames(runParams(x)))
stop("The following elements in 'params' are not columns in",
" runParams (x) ",
paste(badParams, collapse = ",")
)
}
## Subset 'runParams' based on items in 'params'
newRunParams <- runParams(x)
for (i in names(params)) {
newRunParams <-
subset(newRunParams, newRunParams[, i] %in% params[[i]])
if (nrow(newRunParams) == 0) {
stop("No runs matched the criteria given in 'params'. Check",
" 'runParams(x)' for complete list of parameters used",
" to generate 'x'.")
}
}
## Get index of selected models, subset celdaList, and return
ix <- match(newRunParams$index, runParams(x)$index)
if (length(ix) == 1) {
return(resList(x)[[ix]])
} else {
x@runParams <- as.data.frame(newRunParams)
x@resList <- resList(x)[ix]
return(x)
}
}
)
#' @title Select best chain within each combination of parameters
#' @description Select the chain with the best log likelihood for each
#' combination of tested parameters from a \code{SCE} object gererated by
#' \link{celdaGridSearch} or from a \code{celdaList} object.
#' @param x Can be one of
#' \itemize{
#' \item A \linkS4class{SingleCellExperiment} object returned from
#' \code{celdaGridSearch}, \code{recursiveSplitModule},
#' or \code{recursiveSplitCell}. Must contain a list named
#' \code{"celda_grid_search"} in \code{metadata(x)}.
#' \item celdaList object.}
#' @param asList \code{TRUE} or \code{FALSE}. Whether to return the
#' best model as a
#' \code{celdaList} object or not. If \code{FALSE}, return the best model as a
#' corresponding celda model object.
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return One of
#' \itemize{
#' \item A new \linkS4class{SingleCellExperiment} object containing
#' one model with the best log-likelihood for each set of parameters in
#' \code{metadata(x)}. If there is only one set of parameters,
#' a new \linkS4class{SingleCellExperiment} object
#' with the matching model stored in the
#' \link{metadata}
#' \code{"celda_parameters"} slot will be returned. Otherwise, a new
#' \linkS4class{SingleCellExperiment} object with the subset models stored
#' in the \link{metadata}
#' \code{"celda_grid_search"} slot will be returned.
#' \item A new \code{celdaList} object containing one model with the best
#' log-likelihood for each set of parameters. If only one set of parameters
#' is in the \code{celdaList}, the best model will be returned directly
#' instead of a \code{celdaList} object.}
#' @seealso \link{celdaGridSearch} \link{subsetCeldaList}
#' @export
setGeneric("selectBestModel", function(x, ...) {
standardGeneric("selectBestModel")})
#' @rdname selectBestModel
#' @examples
#' data(sceCeldaCGGridSearch)
#' ## Returns same result as running celdaGridSearch with "bestOnly = TRUE"
#' sce <- selectBestModel(sceCeldaCGGridSearch)
#' @importFrom data.table as.data.table
#' @export
setMethod("selectBestModel", signature(x = "SingleCellExperiment"),
function(x, asList = FALSE, altExpName = "featureSubset") {
altExp <- SingleCellExperiment::altExp(x, altExpName)
logLikelihood <- NULL
group <- setdiff(colnames(runParams(x, altExpName = altExpName)),
c("index", "chain", "logLikelihood", "mean_perplexity", "seed"))
runParams <- S4Vectors::metadata(altExp)$celda_grid_search@runParams
dt <- data.table::as.data.table(runParams)
newRunParams <- as.data.frame(dt[, .SD[which.max(logLikelihood)],
by = group])
newRunParams <- newRunParams[, colnames(runParams)]
ix <- match(newRunParams$index, runParams$index)
if (nrow(newRunParams) == 1 & !asList) {
altExp <- .subsetCeldaListSCE(altExp, ix)
} else {
altExp@metadata$celda_grid_search@runParams <-
as.data.frame(newRunParams)
altExp@metadata$celda_grid_search@resList <-
altExp@metadata$celda_grid_search@resList[ix]
}
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname selectBestModel
#' @examples
#' data(celdaCGGridSearchRes)
#' ## Returns same result as running celdaGridSearch with "bestOnly = TRUE"
#' cgsBest <- selectBestModel(celdaCGGridSearchRes)
#' @importFrom data.table as.data.table
#' @export
setMethod("selectBestModel", signature(x = "celdaList"),
function(x, asList = FALSE) {
logLikelihood <- NULL
group <- setdiff(colnames(runParams(x)),
c("index", "chain", "logLikelihood", "mean_perplexity", "seed"))
dt <- data.table::as.data.table(runParams(x))
newRunParams <- as.data.frame(dt[, .SD[which.max(logLikelihood)],
by = group])
newRunParams <- newRunParams[, colnames(runParams(x))]
ix <- match(newRunParams$index, runParams(x)$index)
if (nrow(newRunParams) == 1 & !asList) {
return(resList(x)[[ix]])
} else {
x@runParams <- as.data.frame(newRunParams)
x@resList <- resList(x)[ix]
return(x)
}
}
)
.createSCEceldaGridSearch <- function(celdaList,
sce,
xClass,
useAssay,
model,
paramsTest,
paramsFixed,
maxIter,
seed,
nchains,
cores,
bestOnly,
perplexity,
verbose,
logfilePrefix) {
S4Vectors::metadata(sce)[["celda_grid_search"]] <- celdaList
S4Vectors::metadata(sce)$celda_grid_search@celdaGridSearchParameters <-
list(xClass = xClass,
useAssay = useAssay,
model = model,
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
seed = seed,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
return(sce)
}
.subsetCeldaListSCE <- function(x, ix) {
cgsparam <- x@metadata$celda_grid_search@celdaGridSearchParameters
if (cgsparam$model == "celda_C") {
x <- .createSCEceldaC(celdaCMod =
x@metadata$celda_grid_search@resList[[ix]],
sce = x,
xClass = cgsparam$xClass,
useAssay = cgsparam$useAssay,
algorithm = cgsparam$algorithm,
stopIter = cgsparam$stopIter,
maxIter = cgsparam$maxIter,
splitOnIter = cgsparam$splitOnIter,
splitOnLast = cgsparam$splitOnLast,
nchains = cgsparam$nchains,
zInitialize = cgsparam[["zInitialize"]],
zInit = cgsparam[["zInit"]],
logfile = cgsparam$logfile,
verbose = cgsparam$verbose)
} else if (cgsparam$model == "celda_G") {
x <- .createSCEceldaG(celdaGMod =
x@metadata$celda_grid_search@resList[[ix]],
sce = x,
xClass = cgsparam$xClass,
useAssay = cgsparam$useAssay,
stopIter = cgsparam$stopIter,
maxIter = cgsparam$maxIter,
splitOnIter = cgsparam$splitOnIter,
splitOnLast = cgsparam$splitOnLast,
nchains = cgsparam$nchains,
yInitialize = cgsparam[["yInitialize"]],
yInit = cgsparam[["yInit"]],
logfile = cgsparam$logfile,
verbose = cgsparam$verbose)
} else if (cgsparam$model == "celda_CG") {
x <- .createSCEceldaCG(celdaCGMod =
x@metadata$celda_grid_search@resList[[ix]],
sce = x,
xClass = cgsparam$xClass,
useAssay = cgsparam$useAssay,
algorithm = cgsparam$algorithm,
stopIter = cgsparam$stopIter,
maxIter = cgsparam$maxIter,
splitOnIter = cgsparam$splitOnIter,
splitOnLast = cgsparam$splitOnLast,
nchains = cgsparam$nchains,
zInitialize = cgsparam[["zInitialize"]],
yInitialize = cgsparam[["yInitialize"]],
zInit = cgsparam[["zInit"]],
yInit = cgsparam[["yInit"]],
logfile = cgsparam$logfile,
verbose = cgsparam$verbose)
} else {
stop("S4Vectors::metadata(altExp(x, altExpName))$celda_grid_search@",
"celdaGridSearchParameters$model must be",
" one of 'celda_C', 'celda_G', or 'celda_CG'")
}
return(x)
}
Try the celda package in your browser
Any scripts or data that you put into this service are public.
celda documentation built on Nov. 8, 2020, 8:24 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions .subsetCeldaListSCE .createSCEceldaGridSearch .celdaGridSearch
#' @title Run Celda in parallel with multiple parameters
#' @description Run Celda with different combinations of parameters and
#' multiple chains in parallel. The variable \link{availableModels} contains
#' the potential models that can be utilized. Different parameters to be tested
#' should be stored in a list and passed to the argument \code{paramsTest}.
#' Fixed parameters to be used in all models, such as \code{sampleLabel}, can
#' be passed as a list to the argument \code{paramsFixed}. When
#' \code{verbose = TRUE}, output from each chain will be sent to a log file
#' but not be displayed in \code{stdout}.
#' @param x A numeric \link{matrix} of counts or a
#' \linkS4class{SingleCellExperiment}
#' with the matrix located in the assay slot under \code{useAssay}.
#' Rows represent features and columns represent cells.
#' @param useAssay A string specifying the name of the
#' \link{assay} slot to use. Default "counts".
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param model Celda model. Options available in \link{availableModels}.
#' @param paramsTest List. A list denoting the combinations of parameters to
#' run in a celda model. For example,
#' \code{list(K = seq(5, 10), L = seq(15, 20))}
#' will run all combinations of K from 5 to 10 and L from 15 to 20 in model
#' \link{celda_CG}.
#' @param paramsFixed List. A list denoting additional parameters to use in
#' each celda model. Default NULL.
#' @param maxIter Integer. Maximum number of iterations of sampling to
#' perform. Default 200.
#' @param nchains Integer. Number of random cluster initializations. Default 3.
#' @param cores Integer. The number of cores to use for parallel estimation of
#' chains. Default 1.
#' @param bestOnly Logical. Whether to return only the chain with the highest
#' log likelihood per combination of parameters or return all chains. Default
#' TRUE.
#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
#' a default value of 12345 is used. Seed values
#' \code{seq(seed, (seed + nchains - 1))} will be supplied to each chain in
#' \code{nchains}. If NULL, no calls to
#' \link[withr]{with_seed} are made.
#' @param perplexity Logical. Whether to calculate perplexity for each model.
#' If FALSE, then perplexity can be calculated later with
#' \link{resamplePerplexity}. Default TRUE.
#' @param verbose Logical. Whether to print log messages during celda chain
#' execution. Default TRUE.
#' @param logfilePrefix Character. Prefix for log files from worker threads
#' and main process. Default "Celda".
#' @return A \linkS4class{SingleCellExperiment} object. Function
#' parameter settings and celda model results are stored in the
#' \link{metadata} \code{"celda_grid_search"} slot.
#' @param ... Ignored. Placeholder to prevent check warning.
#' @seealso \link{celda_G} for feature clustering, \link{celda_C} for
#' clustering of cells, and \link{celda_CG} for simultaneous clustering of
#' features and cells. \link{subsetCeldaList} can subset the \code{celdaList}
#' object. \link{selectBestModel} can get the best model for each combination
#' of parameters.
#' @import foreach
#' @importFrom doParallel registerDoParallel
#' @importFrom methods is
#' @examples
#' \dontrun{
#' data(celdaCGSim)
#' ## Run various combinations of parameters with 'celdaGridSearch'
#' celdaCGGridSearchRes <- celdaGridSearch(celdaCGSim$counts,
#' model = "celda_CG",
#' paramsTest = list(K = seq(4, 6), L = seq(9, 11)),
#' paramsFixed = list(sampleLabel = celdaCGSim$sampleLabel),
#' bestOnly = TRUE,
#' nchains = 1,
#' cores = 1)
#' }
#' @export
setGeneric("celdaGridSearch", function(x, ...) {
standardGeneric("celdaGridSearch")})
#' @rdname celdaGridSearch
#' @export
setMethod("celdaGridSearch",
signature(x = "SingleCellExperiment"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
model,
paramsTest,
paramsFixed = NULL,
maxIter = 200,
nchains = 3,
cores = 1,
bestOnly = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfilePrefix = "Celda") {
xClass <- "SingleCellExperiment"
if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {
stop(altExpName, " not in 'altExpNames(x)'. Run ",
"selectFeatures(x) first!")
}
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {
stop(useAssay, " not in assayNames(altExp(x, altExpName))")
}
counts <- SummarizedExperiment::assay(altExp, i = useAssay)
celdaList <- .celdaGridSearch(counts = counts,
model = paste0(".", model),
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
altExp <- .createSCEceldaGridSearch(celdaList = celdaList,
sce = altExp,
xClass = xClass,
useAssay = useAssay,
model = model,
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
seed = seed,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
})
#' @rdname celdaGridSearch
#' @export
setMethod("celdaGridSearch",
signature(x = "matrix"),
function(x,
useAssay = "counts",
altExpName = "featureSubset",
model,
paramsTest,
paramsFixed = NULL,
maxIter = 200,
nchains = 3,
cores = 1,
bestOnly = TRUE,
seed = 12345,
perplexity = TRUE,
verbose = TRUE,
logfilePrefix = "Celda") {
ls <- list()
ls[[useAssay]] <- x
sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)
SingleCellExperiment::altExp(sce, altExpName) <- sce
xClass <- "matrix"
celdaList <- .celdaGridSearch(counts = x,
model = paste0(".", model),
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
seed = seed,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
altExp <- .createSCEceldaGridSearch(celdaList = celdaList,
sce = SingleCellExperiment::altExp(sce, altExpName),
xClass = xClass,
useAssay = useAssay,
model = model,
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
seed = seed,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
SingleCellExperiment::altExp(sce, altExpName) <- altExp
return(sce)
})
.celdaGridSearch <- function(counts,
model,
paramsTest,
paramsFixed,
maxIter,
nchains,
cores,
bestOnly,
seed,
perplexity,
verbose,
logfilePrefix) {
## Check parameters
.validateCounts(counts)
modelParams <- as.list(formals(model))
if (!all(names(paramsTest) %in% names(modelParams))) {
badParams <- setdiff(names(paramsTest), names(modelParams))
stop(
"The following elements in 'paramsTest' are not arguments of '",
substring(model, 2),
"': ",
paste(badParams, collapse = ",")
)
}
if (!is.null(paramsFixed) &&
!all(names(paramsFixed) %in% names(modelParams))) {
badParams <- setdiff(names(paramsFixed), names(modelParams))
stop(
"The following elements in 'paramsFixed' are not arguments",
" of '",
substring(model, 2),
"': ",
paste(badParams, collapse = ",")
)
}
modelParamsRequired <- setdiff(
names(modelParams[modelParams == ""]),
"counts"
)
if (!all(modelParamsRequired %in% c(
names(paramsTest),
names(paramsFixed)
))) {
missing.params <- setdiff(
modelParamsRequired,
c(names(paramsTest), names(paramsFixed))
)
stop(
"The following arguments are not in 'paramsTest' or 'paramsFixed'",
" but are required for '",
substring(model, 2),
"': ",
paste(missing.params, collapse = ",")
)
}
if (any(c("z.init", "y.init", "sampleLabel") %in% names(paramsTest))) {
stop(
"Setting parameters such as 'z.init', 'y.init', and 'sampleLabel'",
" in 'paramsTest' is not currently supported."
)
}
if (any(c("nchains") %in% names(paramsTest))) {
warning(
"Parameter 'nchains' should not be used within the paramsTest",
" list"
)
paramsTest[["nchains"]] <- NULL
}
# Pre-generate a set of random seeds to be used for each chain
if (is.null(seed)) {
allSeeds <- NULL
} else {
allSeeds <- seq(seed, (seed + nchains - 1))
}
# Set up parameter combinations for each individual chain
runParams <- base::expand.grid(c(
chain = list(seq_len(nchains)),
paramsTest
))
runParams <- cbind(index = seq_len(nrow(runParams)), runParams)
if (is.null(allSeeds)) {
runParams <- cbind(runParams,
seed = rep("NULL", nrow(runParams)))
} else {
runParams <- cbind(runParams,
seed = rep(allSeeds, nrow(runParams) / nchains))
}
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = FALSE,
verbose = verbose
)
.logMessages("Starting celdaGridSearch with",
substring(model, 2),
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages("Number of cores:",
cores,
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = TRUE,
verbose = verbose
)
startTime <- Sys.time()
# An MD5 checksum of the count matrix. Passed to models so
# later on, we can check on celda_* model objects which
# count matrix was used.
counts <- .processCounts(counts)
countChecksum <- .createCountChecksum(counts)
## Use DoParallel to loop through each combination of parameters
cl <- parallel::makeCluster(cores)
doParallel::registerDoParallel(cl)
i <- NULL # Setting visible binding for R CMD CHECK
resList <- foreach(
i = seq_len(nrow(runParams)),
.export = model,
.combine = c,
.multicombine = TRUE
) %dopar% {
## Set up chain parameter list
current.run <- c(runParams[i, ])
chainParams <- list()
for (j in names(paramsTest)) {
chainParams[[j]] <- current.run[[j]]
}
chainParams$counts <- counts
chainParams$maxIter <- maxIter
chainParams$nchain <- 1
chainParams$countChecksum <- countChecksum
chainParams$verbose <- verbose
chainParams$logfile <- paste0(
logfilePrefix,
"_",
paste(paste(
colnames(runParams), runParams[i, ],
sep = "-"
), collapse = "_"),
"_Seed-",
ifelse(is.null(chainParams$seed), "NULL", chainParams$seed),
"_log.txt"
)
## Run model
if (is.null(seed)) {
res <- do.call(model, c(chainParams, paramsFixed))
} else {
chainSeed <- allSeeds[ifelse(i %% nchains == 0,
nchains, i %% nchains)]
res <- with_seed(chainSeed,
do.call(model, c(chainParams, paramsFixed)))
}
return(list(res))
}
parallel::stopCluster(cl)
logliks <- vapply(resList, function(mod) {
bestLogLikelihood(mod)
}, double(1))
runParams <- cbind(runParams, logLikelihood = logliks)
celdaRes <- methods::new(
"celdaList",
runParams = runParams,
resList = resList,
countChecksum = countChecksum
)
if (isTRUE(bestOnly)) {
celdaRes <- selectBestModel(celdaRes, asList = TRUE)
}
if (isTRUE(perplexity)) {
.logMessages(
date(),
".. Calculating perplexity",
append = TRUE,
verbose = verbose,
logfile = NULL
)
celdaRes <- resamplePerplexity(counts, celdaRes, seed = seed)
}
endTime <- Sys.time()
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages("Completed celdaGridSearch. Total time:",
format(difftime(endTime, startTime)),
logfile = NULL,
append = TRUE,
verbose = verbose
)
.logMessages(paste(rep("-", 50), collapse = ""),
logfile = NULL,
append = TRUE,
verbose = verbose
)
return(celdaRes)
}
#' @title Subset celda model from SCE object returned from
#' \code{celdaGridSearch}
#' @description Select a subset of models from a
#' \linkS4class{SingleCellExperiment} object generated by
#' \link{celdaGridSearch} that match the criteria in the argument
#' \code{params}.
#' @param x Can be one of
#' \itemize{
#' \item A \linkS4class{SingleCellExperiment} object returned from
#' \code{celdaGridSearch}, \code{recursiveSplitModule},
#' or \code{recursiveSplitCell}. Must contain a list named
#' \code{"celda_grid_search"} in \code{metadata(x)}.
#' \item celdaList object.}
#' @param params List. List of parameters used to subset the matching celda
#' models in list \code{"celda_grid_search"} in \code{metadata(x)}.
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return One of
#' \itemize{
#' \item A new \linkS4class{SingleCellExperiment} object containing
#' all models matching the
#' provided criteria in \code{params}. If only one celda model result in the
#' \code{"celda_grid_search"} slot in \code{metadata(x)} matches
#' the given criteria, a new \linkS4class{SingleCellExperiment} object
#' with the matching model stored in the
#' \link{metadata}
#' \code{"celda_parameters"} slot will be returned. Otherwise, a new
#' \linkS4class{SingleCellExperiment} object with the subset models stored
#' in the \link{metadata}
#' \code{"celda_grid_search"} slot will be returned.
#' \item A new \code{celdaList} object containing all models matching the
#' provided criteria in \code{params}. If only one item in the
#' \code{celdaList} matches the given criteria, the matching model will be
#' returned directly instead of a \code{celdaList} object.}
#' @seealso \link{celdaGridSearch} can run Celda with multiple parameters and
#' chains in parallel. \link{selectBestModel} can get the best model for each
#' combination of parameters.
#' @export
setGeneric("subsetCeldaList", function(x, ...) {
standardGeneric("subsetCeldaList")})
#' @rdname subsetCeldaList
#' @examples
#' data(sceCeldaCGGridSearch)
#' sceK5L10 <- subsetCeldaList(sceCeldaCGGridSearch,
#' params = list(K = 5, L = 10))
#' @export
setMethod("subsetCeldaList",
signature(x = "SingleCellExperiment"),
function(x, params, altExpName = "featureSubset") {
## Check for bad parameter names
if (!all(names(params) %in% colnames(runParams(x,
altExpName = altExpName)))) {
badParams <- setdiff(names(params),
colnames(runParams(x, altExpName = altExpName)))
stop("The following elements in 'params' are not columns in",
" runParams(x, altExpName = altExpName) ",
paste(badParams, collapse = ",")
)
}
## Subset 'runParams' based on items in 'params'
newRunParams <- runParams(x, altExpName = altExpName)
for (i in names(params)) {
newRunParams <-
subset(newRunParams, newRunParams[, i] %in% params[[i]])
if (nrow(newRunParams) == 0) {
stop("No runs matched the criteria given in 'params'. Check",
" 'runParams(x, altExpName = altExpName)' for complete",
" list of parameters used",
" to generate 'x'.")
}
}
## Get index of selected models, subset celdaList, and return
ix <- match(newRunParams$index, runParams(x,
altExpName = altExpName)$index)
altExp <- SingleCellExperiment::altExp(x, altExpName)
if (length(ix) == 1) {
altExp <- .subsetCeldaListSCE(altExp, ix)
} else {
altExp@metadata$celda_grid_search@runParams <-
as.data.frame(newRunParams)
altExp@metadata$celda_grid_search@resList <-
altExp@metadata$celda_grid_search@resList[ix]
}
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname subsetCeldaList
#' @examples
#' data(celdaCGGridSearchRes)
#' resK5L10 <- subsetCeldaList(celdaCGGridSearchRes,
#' params = list(K = 5, L = 10))
#' @export
setMethod("subsetCeldaList",
signature(x = "celdaList"),
function(x, params) {
## Check for bad parameter names
if (!all(names(params) %in% colnames(runParams(x)))) {
badParams <- setdiff(names(params), colnames(runParams(x)))
stop("The following elements in 'params' are not columns in",
" runParams (x) ",
paste(badParams, collapse = ",")
)
}
## Subset 'runParams' based on items in 'params'
newRunParams <- runParams(x)
for (i in names(params)) {
newRunParams <-
subset(newRunParams, newRunParams[, i] %in% params[[i]])
if (nrow(newRunParams) == 0) {
stop("No runs matched the criteria given in 'params'. Check",
" 'runParams(x)' for complete list of parameters used",
" to generate 'x'.")
}
}
## Get index of selected models, subset celdaList, and return
ix <- match(newRunParams$index, runParams(x)$index)
if (length(ix) == 1) {
return(resList(x)[[ix]])
} else {
x@runParams <- as.data.frame(newRunParams)
x@resList <- resList(x)[ix]
return(x)
}
}
)
#' @title Select best chain within each combination of parameters
#' @description Select the chain with the best log likelihood for each
#' combination of tested parameters from a \code{SCE} object gererated by
#' \link{celdaGridSearch} or from a \code{celdaList} object.
#' @param x Can be one of
#' \itemize{
#' \item A \linkS4class{SingleCellExperiment} object returned from
#' \code{celdaGridSearch}, \code{recursiveSplitModule},
#' or \code{recursiveSplitCell}. Must contain a list named
#' \code{"celda_grid_search"} in \code{metadata(x)}.
#' \item celdaList object.}
#' @param asList \code{TRUE} or \code{FALSE}. Whether to return the
#' best model as a
#' \code{celdaList} object or not. If \code{FALSE}, return the best model as a
#' corresponding celda model object.
#' @param altExpName The name for the \link{altExp} slot
#' to use. Default "featureSubset".
#' @param ... Ignored. Placeholder to prevent check warning.
#' @return One of
#' \itemize{
#' \item A new \linkS4class{SingleCellExperiment} object containing
#' one model with the best log-likelihood for each set of parameters in
#' \code{metadata(x)}. If there is only one set of parameters,
#' a new \linkS4class{SingleCellExperiment} object
#' with the matching model stored in the
#' \link{metadata}
#' \code{"celda_parameters"} slot will be returned. Otherwise, a new
#' \linkS4class{SingleCellExperiment} object with the subset models stored
#' in the \link{metadata}
#' \code{"celda_grid_search"} slot will be returned.
#' \item A new \code{celdaList} object containing one model with the best
#' log-likelihood for each set of parameters. If only one set of parameters
#' is in the \code{celdaList}, the best model will be returned directly
#' instead of a \code{celdaList} object.}
#' @seealso \link{celdaGridSearch} \link{subsetCeldaList}
#' @export
setGeneric("selectBestModel", function(x, ...) {
standardGeneric("selectBestModel")})
#' @rdname selectBestModel
#' @examples
#' data(sceCeldaCGGridSearch)
#' ## Returns same result as running celdaGridSearch with "bestOnly = TRUE"
#' sce <- selectBestModel(sceCeldaCGGridSearch)
#' @importFrom data.table as.data.table
#' @export
setMethod("selectBestModel", signature(x = "SingleCellExperiment"),
function(x, asList = FALSE, altExpName = "featureSubset") {
altExp <- SingleCellExperiment::altExp(x, altExpName)
logLikelihood <- NULL
group <- setdiff(colnames(runParams(x, altExpName = altExpName)),
c("index", "chain", "logLikelihood", "mean_perplexity", "seed"))
runParams <- S4Vectors::metadata(altExp)$celda_grid_search@runParams
dt <- data.table::as.data.table(runParams)
newRunParams <- as.data.frame(dt[, .SD[which.max(logLikelihood)],
by = group])
newRunParams <- newRunParams[, colnames(runParams)]
ix <- match(newRunParams$index, runParams$index)
if (nrow(newRunParams) == 1 & !asList) {
altExp <- .subsetCeldaListSCE(altExp, ix)
} else {
altExp@metadata$celda_grid_search@runParams <-
as.data.frame(newRunParams)
altExp@metadata$celda_grid_search@resList <-
altExp@metadata$celda_grid_search@resList[ix]
}
SingleCellExperiment::altExp(x, altExpName) <- altExp
return(x)
}
)
#' @rdname selectBestModel
#' @examples
#' data(celdaCGGridSearchRes)
#' ## Returns same result as running celdaGridSearch with "bestOnly = TRUE"
#' cgsBest <- selectBestModel(celdaCGGridSearchRes)
#' @importFrom data.table as.data.table
#' @export
setMethod("selectBestModel", signature(x = "celdaList"),
function(x, asList = FALSE) {
logLikelihood <- NULL
group <- setdiff(colnames(runParams(x)),
c("index", "chain", "logLikelihood", "mean_perplexity", "seed"))
dt <- data.table::as.data.table(runParams(x))
newRunParams <- as.data.frame(dt[, .SD[which.max(logLikelihood)],
by = group])
newRunParams <- newRunParams[, colnames(runParams(x))]
ix <- match(newRunParams$index, runParams(x)$index)
if (nrow(newRunParams) == 1 & !asList) {
return(resList(x)[[ix]])
} else {
x@runParams <- as.data.frame(newRunParams)
x@resList <- resList(x)[ix]
return(x)
}
}
)
.createSCEceldaGridSearch <- function(celdaList,
sce,
xClass,
useAssay,
model,
paramsTest,
paramsFixed,
maxIter,
seed,
nchains,
cores,
bestOnly,
perplexity,
verbose,
logfilePrefix) {
S4Vectors::metadata(sce)[["celda_grid_search"]] <- celdaList
S4Vectors::metadata(sce)$celda_grid_search@celdaGridSearchParameters <-
list(xClass = xClass,
useAssay = useAssay,
model = model,
paramsTest = paramsTest,
paramsFixed = paramsFixed,
maxIter = maxIter,
seed = seed,
nchains = nchains,
cores = cores,
bestOnly = bestOnly,
perplexity = perplexity,
verbose = verbose,
logfilePrefix = logfilePrefix)
return(sce)
}
.subsetCeldaListSCE <- function(x, ix) {
cgsparam <- x@metadata$celda_grid_search@celdaGridSearchParameters
if (cgsparam$model == "celda_C") {
x <- .createSCEceldaC(celdaCMod =
x@metadata$celda_grid_search@resList[[ix]],
sce = x,
xClass = cgsparam$xClass,
useAssay = cgsparam$useAssay,
algorithm = cgsparam$algorithm,
stopIter = cgsparam$stopIter,
maxIter = cgsparam$maxIter,
splitOnIter = cgsparam$splitOnIter,
splitOnLast = cgsparam$splitOnLast,
nchains = cgsparam$nchains,
zInitialize = cgsparam[["zInitialize"]],
zInit = cgsparam[["zInit"]],
logfile = cgsparam$logfile,
verbose = cgsparam$verbose)
} else if (cgsparam$model == "celda_G") {
x <- .createSCEceldaG(celdaGMod =
x@metadata$celda_grid_search@resList[[ix]],
sce = x,
xClass = cgsparam$xClass,
useAssay = cgsparam$useAssay,
stopIter = cgsparam$stopIter,
maxIter = cgsparam$maxIter,
splitOnIter = cgsparam$splitOnIter,
splitOnLast = cgsparam$splitOnLast,
nchains = cgsparam$nchains,
yInitialize = cgsparam[["yInitialize"]],
yInit = cgsparam[["yInit"]],
logfile = cgsparam$logfile,
verbose = cgsparam$verbose)
} else if (cgsparam$model == "celda_CG") {
x <- .createSCEceldaCG(celdaCGMod =
x@metadata$celda_grid_search@resList[[ix]],
sce = x,
xClass = cgsparam$xClass,
useAssay = cgsparam$useAssay,
algorithm = cgsparam$algorithm,
stopIter = cgsparam$stopIter,
maxIter = cgsparam$maxIter,
splitOnIter = cgsparam$splitOnIter,
splitOnLast = cgsparam$splitOnLast,
nchains = cgsparam$nchains,
zInitialize = cgsparam[["zInitialize"]],
yInitialize = cgsparam[["yInitialize"]],
zInit = cgsparam[["zInit"]],
yInit = cgsparam[["yInit"]],
logfile = cgsparam$logfile,
verbose = cgsparam$verbose)
} else {
stop("S4Vectors::metadata(altExp(x, altExpName))$celda_grid_search@",
"celdaGridSearchParameters$model must be",
" one of 'celda_C', 'celda_G', or 'celda_CG'")
}
return(x)
}
Try the celda package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.